If it is a .net application then you should be able to run it without wine. Open a new terminal window and type:
If you don't have mono installed then do
mono <path to file>
(I think that is the right package, not 100% sure, though)
sudo apt-get install mono-runtime
Don't be fooled into thinking that a .exe can only be run in wine, that is also the file extension for .net applications. I learned that the hard way.
For copying/pasting in terminal the keyboard shortcuts have a shift in them. Copy = ctrl+shift+c Paste = ctrl+shift+v